Medical procedures such as endoscopy (e.g., bronchoscopy) may involve accessing and visualizing the inside of a patient's lumen (e.g., airways) for diagnostic and/or therapeutic purposes. During a procedure a flexible tubular tool such as, for example, an endoscope, may be inserted into the patient's body and an instrument can be passed through the endoscope to a tissue site identified for diagnosis and/or treatment. For example, the endoscope can have an interior lumen (e.g., “working channel”) providing a pathway to the tissue site, wherein various tools/instruments can be inserted through the interior lumen to the tissue site. A robotic system may be used to control the insertion and/or manipulation of the endoscope and/or the tools/instruments during the procedure, and may comprise at least one robotic arm that includes a manipulator assembly configured to control the positioning of the endoscope and/or tools/instrument during the procedure.